COVID-19 diagnosis -A review of current methods

Abstract

A fast and accurate self-testing tool for COVID-19 diagnosis has become a prerequisite to comprehend the exact number of cases worldwide and to take medical and governmental actions accordingly. SARS-CoV-2 (formerly, 2019-nCoV) infection was first reported in Wuhan (China) in December 2019, and then it has rapidly spread around the world, causing _~14 million active cases with _~582,000 deaths as of July 2020. The diagnosis tools available so far have been based on a) viral gene detection, b) human antibody detection, and c) viral antigen detection, among which the viral gene detection by RT-PCR has been found as the most reliable technique. In this report, the current SARS-CoV-2 detection kits, exclusively the ones that were issued an "Emergency Use Authorization" from the U.S. Food and Drug Administration, were discussed. The key structural components of the virus were presented to provide the audience with an understanding of the scientific principles behind the testing tools. The methods that are still in the early research state were also reviewed in a subsection based on the reports available so far.

Keywords: COVID-19; Lateral flow assay; Loop-mediated isothermal amplification; Point of care devices; RT-PCR; SARS-CoV-2 detection; SARS-CoV-2 diagnosis.

Fig. 1

A visual artwork for whole SARS-CoV-2 virus (a), cryo-EM restructure of SARS-CoV-2 S trimer glycoprotein, which is responsible for host cell receptor binding (b), and the complete genome structure of SARS-CoV-2 virus (c). a) The morphological structure of SARS-Cov-2 reproduced from ref (Rosales-Mendoza et al., 2020). “The envelope membrane is associated with the spike protein (S), which mediates binding to the host cell receptors and considered a critical target for the induction of antibodies capable of neutralizing the virus; hemagglutinin-esterase dimer (HE), which acts as a potent mediator of attachment and destruction of sialic acid receptors on the host cell surface; a membrane glycoprotein (M), which is important to generate the virus; and the envelope protein (E), which adheres to the M protein to form the viral envelope. The viral structure also comprises a nucleocapsid protein (N) that, along with the RNA genome, produces the nucleocapsid.” (Rosales-Mendoza et al., 2020). b) The reconstruction of the closed SARS-CoV-2 S ectodomain trimer at 2.8Å resolution reproduced from ref (Walls et al., 2020). “(A) Closed SARS-CoV-2 S trimer unsharpened cryo-EM map. (B and C) Two orthogonal views from the side (B) and top (C) of the atomic model of the closed SARS- CoV-2” (Walls et al., 2020). c) Complete genome structure of the SARS-CoV-2 virus, the data is redrawn based on the information and results of ref (Khailany et al., 2020).

Fig. 2

The principle of RT-PCR based on commercial TaqMan probes (a) and the relative amplicon positions for SARS-Cov-2 on GenBank data of the previous SARS-CoV and SARS-CoV-2 (b). a) TagMan Probe-based RT-PCR steps. The illustration was redrawn based on Ref (Roy et al., 2019). The probe is modified with a fluorescent dye (reporter dye) at one end, and one quencher dye on the other end. The quencher blocks the fluorescent signal of the reporter dye due to proximity. The probe does not fluoresce in its native condition. When the polymerase enzyme starts the amplification and encounters with the labeled probe, the probe gets hydrolyzed, releasing its components away from each other, which constitutes a fluorescent signal. Each successful amplification produces fluorescent that is proportional to the amount of the target gene in the sample. b) Relative positions of amplicon targets on SARS-CoV and Wuhan-CoV genome. S: Spike glycoprotein, E: Envelope protein, M: Membrane protein, N: nucleocapsid; ORF: open reading frame; RdRp: RNA-dependent RNA polymerase. Numbers below amplicon are genome positions according to SARS-CoV, NC_004718”. Reproduced from ref (Corman et al., 2020).

Fig. 3

(a) Illustration of the method workflow. Standard RNA extraction solution or original sample matrix can be used as an input to detect E, N, and RNase P genes. The assay is monitored by a fluorescent reader or lateral flow strip. (b) Lateral flow readout of SARS-CoV-2 positive sample. Detection of at least two genes is necessary for positive sample confirmation. Reproduced from ref (Broughton et al., 2020).